TB-Profiler result

Run: ERR11067724
Summary

Run ID: ERR11067724

Sample name:

Date: 05-04-2023 07:03:51

Number of reads: 2536056

Percentage reads mapped: 99.38

Strain: lineage4.8;lineage1.2.2.2

Drug-resistance: Pre-XDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 0.16
lineage1 Indo-Oceanic EAI RD239 0.84
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.16
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.84
lineage1.2.2.2 Indo-Oceanic NA RD239 0.85
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
gyrB 6620 p.Asp461Asn missense_variant 0.84 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Gly missense_variant 0.84 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.86 isoniazid, ethionamide
embB 4247431 p.Met306Ile missense_variant 0.89 ethambutol
gid 4408115 c.87delC frameshift_variant 0.85 streptomycin
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrB 5075 c.-165C>T upstream_gene_variant 0.86
gyrB 6112 p.Met291Ile missense_variant 0.83
gyrA 7268 c.-34C>T upstream_gene_variant 0.87
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.85
gyrA 8452 p.Ala384Val missense_variant 0.85
gyrA 9143 c.1842T>C synonymous_variant 0.82
gyrA 9304 p.Gly668Asp missense_variant 0.88
fgd1 491742 c.960T>C synonymous_variant 0.91
mshA 576106 c.759C>G synonymous_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 0.93
rpoC 763884 p.Ala172Val missense_variant 0.87
rpoC 763886 c.517C>A synonymous_variant 0.87
rpoC 764154 p.Gln262Arg missense_variant 0.85
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.84
mmpL5 778992 c.-512C>T upstream_gene_variant 0.83
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.73
atpE 1460992 c.-53A>C upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.28
rpsA 1834027 c.486G>A synonymous_variant 0.74
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918245 c.306C>T synonymous_variant 0.77
katG 2154724 p.Arg463Leu missense_variant 0.88
PPE35 2167926 p.Leu896Ser missense_variant 0.9
PPE35 2168742 p.Gly624Asp missense_variant 0.86
PPE35 2170412 c.201G>A synonymous_variant 0.11
Rv1979c 2222308 p.Asp286Gly missense_variant 0.86
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288835 p.Asp136Val missense_variant 0.86
pncA 2288982 p.Thr87Met missense_variant 0.14
kasA 2518132 c.18C>T synonymous_variant 0.84
ahpC 2726051 c.-142G>A upstream_gene_variant 0.84
ald 3086788 c.-32T>C upstream_gene_variant 0.79
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.88
fprA 3474597 c.591C>A synonymous_variant 0.85
fprA 3474698 p.Asp231Gly missense_variant 0.87
fprA 3475159 p.Asn385Asp missense_variant 0.85
alr 3840764 c.657G>C synonymous_variant 0.18
rpoA 3878641 c.-134C>G upstream_gene_variant 0.24
clpC1 4040517 p.Val63Ala missense_variant 0.84
embC 4240671 p.Thr270Ile missense_variant 0.78
embC 4241042 p.Asn394Asp missense_variant 0.87
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 0.82
embB 4247646 p.Glu378Ala missense_variant 0.82
ubiA 4269387 p.Glu149Asp missense_variant 0.8
aftB 4269606 c.-770T>C upstream_gene_variant 0.77
ethA 4326148 c.1326G>T synonymous_variant 0.87
ethA 4326439 p.Asn345Lys missense_variant 0.88
ethA 4326617 p.Tyr286Ala missense_variant 0.17
ethR 4328030 p.Ala161Gly missense_variant 0.25
whiB6 4338203 p.Arg107Cys missense_variant 0.88
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.89
gid 4407588 c.615A>G synonymous_variant 0.87
gid 4407873 c.330G>T synonymous_variant 0.74